GATK-Teaching: Difference between revisions
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cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml GATK/3.8-0-Java-1.8.0_144<br> | ml GATK/3.8-0-Java-1.8.0_144<br> | ||
java-jar$EBROOTGATK/GenomeAnalysisTK.jar <u>[options]</u><br> | java -jar $EBROOTGATK/GenomeAnalysisTK.jar <u>[options]</u><br> | ||
</div> | </div> | ||
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values. | In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values. | ||
Line 60: | Line 60: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
ml GATK/3.8-0-Java-1.8.0_144 | ml GATK/3.8-0-Java-1.8.0_144 | ||
java-jar$EBROOTGATK/GenomeAnalysisTK.jar -h | java -jar $EBROOTGATK/GenomeAnalysisTK.jar -h | ||
---------------------------------------------------------------------------------- | |||
The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50 | |||
Copyright (c) 2010-2016 The Broad Institute | |||
For support and documentation go to https://software.broadinstitute.org/gatk | |||
[Wed Aug 15 15:22:45 EDT 2018] Executing on Linux 3.10.0-862.9.1.el7.x86_64 amd64 | |||
Java HotSpot(TM) 64-Bit Server VM 1.8.0_144-b01 | |||
---------------------------------------------------------------------------------- | |||
---------------------------------------------------------------------------------- | |||
usage: java -jar GenomeAnalysisTK.jar -T <analysis_type> [-args <arg_file>] [-I <input_file>] [--showFullBamList] [-rbs | |||
<read_buffer_size>] [-rf <read_filter>] [-drf <disable_read_filter>] [-L <intervals>] [-XL <excludeIntervals>] [-isr | |||
<interval_set_rule>] [-im <interval_merging>] [-ip <interval_padding>] [-R <reference_sequence>] [-ndrs] [-maxRuntime | |||
<maxRuntime>] [-maxRuntimeUnits <maxRuntimeUnits>] [-dt <downsampling_type>] [-dfrac <downsample_to_fraction>] [-dcov | |||
<downsample_to_coverage>] [-baq <baq>] [-baqGOP <baqGapOpenPenalty>] [-fixNDN] [-fixMisencodedQuals] | |||
[-allowPotentiallyMisencodedQuals] [-OQ] [-DBQ <defaultBaseQualities>] [-PF <performanceLog>] [-BQSR <BQSR>] [-qq | |||
<quantize_quals>] [-SQQ <static_quantized_quals>] [-DIQ] [-EOQ] [-preserveQ <preserve_qscores_less_than>] | |||
[-globalQScorePrior <globalQScorePrior>] [-secondsBetweenProgressUpdates <secondsBetweenProgressUpdates>] [-S | |||
<validation_strictness>] [-rpr] [-kpr] [-sample_rename_mapping_file <sample_rename_mapping_file>] [-U <unsafe>] | |||
[-jdk_deflater] [-jdk_inflater] [-disable_auto_index_creation_and_locking_when_reading_rods] [-no_cmdline_in_header] | |||
[-sites_only] [-writeFullFormat] [-compress <bam_compression>] [-simplifyBAM] [--disable_bam_indexing] [--generate_md5] | |||
[-nt <num_threads>] [-nct <num_cpu_threads_per_data_thread>] [-mte] [-rgbl <read_group_black_list>] [-ped <pedigree>] | |||
[-pedString <pedigreeString>] [-pedValidationType <pedigreeValidationType>] [-variant_index_type <variant_index_type>] | |||
[-variant_index_parameter <variant_index_parameter>] [-ref_win_stop <reference_window_stop>] [-l <logging_level>] [-log | |||
<log_to_file>] [-h] [-version] | |||
-T,--analysis_type <analysis_type> Name of the tool to run | |||
-args,--arg_file <arg_file> Reads arguments from the | |||
specified file | |||
-I,--input_file <input_file> Input file containing sequence | |||
data (BAM or CRAM) | |||
--showFullBamList Emit list of input BAM/CRAM | |||
files to log | |||
-rbs,--read_buffer_size <read_buffer_size> Number of reads per SAM file | |||
to buffer in memory | |||
-rf,--read_filter <read_filter> Filters to apply to reads | |||
before analysis | |||
-drf,--disable_read_filter <disable_read_filter> Read filters to disable | |||
-L,--intervals <intervals> One or more genomic intervals | |||
over which to operate | |||
-XL,--excludeIntervals <excludeIntervals> One or more genomic intervals | |||
to exclude from processing | |||
-isr,--interval_set_rule <interval_set_rule> Set merging approach to use | |||
for combining interval inputs | |||
(UNION|INTERSECTION) | |||
-im,--interval_merging <interval_merging> Interval merging rule for | |||
abutting intervals (ALL| | |||
OVERLAPPING_ONLY) | |||
-ip,--interval_padding <interval_padding> Amount of padding (in bp) to | |||
add to each interval | |||
-R,--reference_sequence <reference_sequence> Reference sequence file | |||
-ndrs,--nonDeterministicRandomSeed Use a non-deterministic random | |||
seed | |||
-maxRuntime,--maxRuntime <maxRuntime> Stop execution cleanly as soon | |||
as maxRuntime has been reached | |||
-maxRuntimeUnits,--maxRuntimeUnits <maxRuntimeUnits> Unit of time used by | |||
maxRuntime (NANOSECONDS| | |||
MICROSECONDS|MILLISECONDS| | |||
SECONDS|MINUTES|HOURS|DAYS) | |||
-dt,--downsampling_type <downsampling_type> Type of read downsampling to | |||
employ at a given locus (NONE| | |||
ALL_READS|BY_SAMPLE) | |||
-dfrac,--downsample_to_fraction <downsample_to_fraction> Fraction of reads to | |||
downsample to | |||
-dcov,--downsample_to_coverage <downsample_to_coverage> Target coverage threshold for | |||
downsampling to coverage | |||
-baq,--baq <baq> Type of BAQ calculation to | |||
apply in the engine (OFF| | |||
CALCULATE_AS_NECESSARY| | |||
RECALCULATE) | |||
-baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty> BAQ gap open penalty | |||
-fixNDN,--refactor_NDN_cigar_string Reduce NDN elements in CIGAR | |||
string | |||
-fixMisencodedQuals,--fix_misencoded_quality_scores Fix mis-encoded base quality | |||
scores | |||
-allowPotentiallyMisencodedQuals,--allow_potentially_misencoded_quality_scores Ignore warnings about base | |||
quality score encoding | |||
-OQ,--useOriginalQualities Use the base quality scores | |||
from the OQ tag | |||
-DBQ,--defaultBaseQualities <defaultBaseQualities> Assign a default base quality | |||
-PF,--performanceLog <performanceLog> Write GATK runtime performance | |||
log to this file | |||
-BQSR,--BQSR <BQSR> Input covariates table file | |||
for on-the-fly base quality | |||
score recalibration | |||
-qq,--quantize_quals <quantize_quals> Quantize quality scores to a | |||
given number of levels (with | |||
-BQSR) | |||
-SQQ,--static_quantized_quals <static_quantized_quals> Use static quantized quality | |||
scores to a given number of | |||
levels (with -BQSR) | |||
-DIQ,--disable_indel_quals Disable printing of base | |||
insertion and deletion tags | |||
(with -BQSR) | |||
-EOQ,--emit_original_quals Emit the OQ tag with the | |||
original base qualities (with | |||
-BQSR) | |||
-preserveQ,--preserve_qscores_less_than <preserve_qscores_less_than> Don't recalibrate bases with | |||
quality scores less than this | |||
threshold (with -BQSR) | |||
-globalQScorePrior,--globalQScorePrior <globalQScorePrior> Global Qscore Bayesian prior | |||
to use for BQSR | |||
-secondsBetweenProgressUpdates,--secondsBetweenProgressUpdates Time interval for process | |||
<secondsBetweenProgressUpdates> meter information output (in | |||
seconds) | |||
-S,--validation_strictness <validation_strictness> How strict should we be with | |||
validation (STRICT|LENIENT| | |||
SILENT) | |||
-rpr,--remove_program_records Remove program records from | |||
the SAM header | |||
-kpr,--keep_program_records Keep program records in the | |||
SAM header | |||
-sample_rename_mapping_file,--sample_rename_mapping_file <sample_rename_mapping_file> Rename sample IDs on-the-fly | |||
at runtime using the provided | |||
mapping file | |||
-U,--unsafe <unsafe> Enable unsafe operations: | |||
nothing will be checked at | |||
runtime (ALLOW_N_CIGAR_READS| | |||
ALLOW_UNINDEXED_BAM| | |||
ALLOW_UNSET_BAM_SORT_ORDER| | |||
NO_READ_ORDER_VERIFICATION| | |||
ALLOW_SEQ_DICT_INCOMPATIBILITY| | |||
LENIENT_VCF_PROCESSING|ALL) | |||
-jdk_deflater,--use_jdk_deflater Use the JDK Deflater instead | |||
of the IntelDeflater for | |||
writing BAMs | |||
-jdk_inflater,--use_jdk_inflater Use the JDK Inflater instead | |||
of the IntelInflater for | |||
reading BAMs | |||
d_locking_when_reading_rods,--disable_auto_index_creation_and_locking_when_reading_rods Disable both auto-generation | |||
of index files and index file | |||
locking | |||
-no_cmdline_in_header,--no_cmdline_in_header Don't include the command line | |||
in output VCF headers | |||
-sites_only,--sites_only Output sites-only VCF | |||
-writeFullFormat,--never_trim_vcf_format_field Always output all the records | |||
in VCF FORMAT fields, even if | |||
some are missing | |||
-compress,--bam_compression <bam_compression> Compression level to use for | |||
writing BAM files (0 - 9, | |||
higher is more compressed) | |||
-simplifyBAM,--simplifyBAM Strip down read content and | |||
tags | |||
--disable_bam_indexing Turn off on-the-fly creation | |||
of indices for output BAM/CRAM | |||
files | |||
--generate_md5 Enable on-the-fly creation of | |||
md5s for output BAM files. | |||
-nt,--num_threads <num_threads> Number of data threads to | |||
allocate to this analysis | |||
-nct,--num_cpu_threads_per_data_thread <num_cpu_threads_per_data_thread> Number of CPU threads to | |||
allocate per data thread | |||
-mte,--monitorThreadEfficiency Enable threading efficiency | |||
monitoring | |||
-rgbl,--read_group_black_list <read_group_black_list> Exclude read groups based on | |||
tags | |||
-ped,--pedigree <pedigree> Pedigree files for samples | |||
-pedString,--pedigreeString <pedigreeString> Pedigree string for samples | |||
-pedValidationType,--pedigreeValidationType <pedigreeValidationType> Validation strictness for | |||
pedigree (STRICT|SILENT) | |||
-variant_index_type,--variant_index_type <variant_index_type> Type of IndexCreator to use | |||
for VCF/BCF indices | |||
(DYNAMIC_SEEK|DYNAMIC_SIZE| | |||
LINEAR|INTERVAL) | |||
-variant_index_parameter,--variant_index_parameter <variant_index_parameter> Parameter to pass to the | |||
VCF/BCF IndexCreator | |||
-ref_win_stop,--reference_window_stop <reference_window_stop> Reference window stop | |||
-l,--logging_level <logging_level> Set the minimum level of | |||
logging | |||
-log,--log_to_file <log_to_file> Set the logging location | |||
-h,--help Generate the help message | |||
-version,--version Output version information | |||
annotator | |||
VariantAnnotator Annotate variant calls with context information | |||
bqsr | |||
AnalyzeCovariates Create plots to visualize base recalibration results | |||
BaseRecalibrator Detect systematic errors in base quality scores | |||
cancer | |||
AssignSomaticStatus Assigns somatic status to a set of calls | |||
contamination | |||
AnnotatePopulationAFWalker Given a input VCF representing a collection of populations, split the input into each | |||
population, and annotate each record with population allele frequencies | |||
ContEst Estimate cross-sample contamination | |||
coverage | |||
CallableLoci Collect statistics on callable, uncallable, poorly mapped, and other parts of the | |||
genome | |||
CompareCallableLoci Compare callability statistics | |||
DepthOfCoverage Assess sequence coverage by a wide array of metrics, partitioned by sample, read group, | |||
or library | |||
GCContentByInterval Calculates the GC content of the reference sequence for each interval | |||
diagnosetargets | |||
DiagnoseTargets Analyze coverage distribution and validate read mates per interval and per sample | |||
diagnostics | |||
ErrorRatePerCycle Compute the read error rate per position | |||
FindCoveredIntervals Outputs a list of intervals that are covered to or above a given threshold | |||
ReadGroupProperties Collect statistics about read groups and their properties | |||
ReadLengthDistribution Collect read length statistics | |||
diffengine | |||
DiffObjects A generic engine for comparing tree-structured objects | |||
examples | |||
GATKPaperGenotyper Simple Bayesian genotyper used in the original GATK paper | |||
fasta | |||
FastaAlternateReferenceMaker Generate an alternative reference sequence over the specified interval | |||
FastaReferenceMaker Create a subset of a FASTA reference sequence | |||
FastaStats Calculate basic statistics about the reference sequence itself | |||
filters | |||
VariantFiltration Filter variant calls based on INFO and FORMAT annotations | |||
genotyper | |||
UnifiedGenotyper Call SNPs and indels on a per-locus basis | |||
haplotypecaller | |||
HaplotypeCaller Call germline SNPs and indels via local re-assembly of haplotypes | |||
HaplotypeResolver Haplotype-based resolution of variants in separate callsets. | |||
indels | |||
IndelRealigner Perform local realignment of reads around indels | |||
LeftAlignIndels Left-align indels within reads in a bam file | |||
RealignerTargetCreator Define intervals to target for local realignment | |||
m2 | |||
MuTect2 Call somatic SNPs and indels via local re-assembly of haplotypes | |||
missing | |||
QualifyMissingIntervals Collect quality metrics for a set of intervals | |||
phasing | |||
PhaseByTransmission Compute the most likely genotype combination and phasing for trios and parent/child | |||
pairs | |||
ReadBackedPhasing Annotate physical phasing information | |||
qc | |||
CheckPileup Compare GATK's internal pileup to a reference Samtools pileup | |||
CountBases Count the number of bases in a set of reads | |||
CountIntervals Count contiguous regions in an interval list | |||
CountLoci Count the total number of covered loci | |||
CountMales Count the number of reads seen from male samples | |||
CountReadEvents Count the number of read events | |||
CountReads Count the number of reads | |||
CountRODs Count the number of ROD objects encountered | |||
CountRODsByRef Count the number of ROD objects encountered along the reference | |||
CountTerminusEvent Count the number of reads ending in insertions, deletions or soft-clips | |||
ErrorThrowing A walker that simply throws errors. | |||
FlagStat Collect statistics about sequence reads based on their SAM flags | |||
Pileup Print read alignments in Pileup-style format | |||
PrintRODs Print out all of the RODs in the input data set | |||
QCRef Quality control for the reference fasta | |||
ReadClippingStats Collect read clipping statistics | |||
readutils | |||
ClipReads Read clipping based on quality, position or sequence matching | |||
PrintReads Write out sequence read data (for filtering, merging, subsetting etc) | |||
SplitSamFile Split a BAM file by sample | |||
rnaseq | |||
ASEReadCounter Calculate read counts per allele for allele-specific expression analysis | |||
SplitNCigarReads Splits reads that contain Ns in their CIGAR string | |||
simulatereads | |||
SimulateReadsForVariants Generate simulated reads for variants | |||
validationsiteselector | |||
ValidationSiteSelector Randomly select variant records according to specified options | |||
varianteval | |||
VariantEval General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv | |||
ratios, and a lot more) | |||
variantrecalibration | |||
ApplyRecalibration Apply a score cutoff to filter variants based on a recalibration table | |||
VariantRecalibrator Build a recalibration model to score variant quality for filtering purposes | |||
variantutils | |||
CalculateGenotypePosteriors Calculate genotype posterior likelihoods given panel data | |||
CombineGVCFs Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file | |||
CombineVariants Combine variant records from different sources | |||
GenotypeConcordance Genotype concordance between two callsets | |||
GenotypeGVCFs Perform joint genotyping on gVCF files produced by HaplotypeCaller | |||
LeftAlignAndTrimVariants Left-align indels in a variant callset | |||
RandomlySplitVariants Randomly split variants into different sets | |||
RegenotypeVariants Regenotypes the variants from a VCF containing PLs or GLs. | |||
SelectHeaders Selects headers from a VCF source | |||
SelectVariants Select a subset of variants from a larger callset | |||
ValidateVariants Validate a VCF file with an extra strict set of criteria | |||
VariantsToAllelicPrimitives Simplify multi-nucleotide variants (MNPs) into more basic/primitive alleles. | |||
VariantsToBinaryPed Convert VCF to binary pedigree file | |||
VariantsToTable Extract specific fields from a VCF file to a tab-delimited table | |||
VariantsToVCF Convert variants from other file formats to VCF format | |||
</pre> | </pre> |
Latest revision as of 15:22, 15 August 2018
Category
Bioinformatics
Program On
Teaching
Version
3.8-0
Author / Distributor
Description
"The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size." More details are at GATK
Running Program
The last version of this application is at /usr/local/apps/eb/GATK/3.8-0-Java-1.8.0_144
To use this version, please load the module with
ml GATK/3.8-0-Java-1.8.0_144
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_GATK
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=GATK.%j.out
#SBATCH --error=GATK.%j.err
cd $SLURM_SUBMIT_DIR
ml GATK/3.8-0-Java-1.8.0_144
java -jar $EBROOTGATK/GenomeAnalysisTK.jar [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml GATK/3.8-0-Java-1.8.0_144 java -jar $EBROOTGATK/GenomeAnalysisTK.jar -h ---------------------------------------------------------------------------------- The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50 Copyright (c) 2010-2016 The Broad Institute For support and documentation go to https://software.broadinstitute.org/gatk [Wed Aug 15 15:22:45 EDT 2018] Executing on Linux 3.10.0-862.9.1.el7.x86_64 amd64 Java HotSpot(TM) 64-Bit Server VM 1.8.0_144-b01 ---------------------------------------------------------------------------------- ---------------------------------------------------------------------------------- usage: java -jar GenomeAnalysisTK.jar -T <analysis_type> [-args <arg_file>] [-I <input_file>] [--showFullBamList] [-rbs <read_buffer_size>] [-rf <read_filter>] [-drf <disable_read_filter>] [-L <intervals>] [-XL <excludeIntervals>] [-isr <interval_set_rule>] [-im <interval_merging>] [-ip <interval_padding>] [-R <reference_sequence>] [-ndrs] [-maxRuntime <maxRuntime>] [-maxRuntimeUnits <maxRuntimeUnits>] [-dt <downsampling_type>] [-dfrac <downsample_to_fraction>] [-dcov <downsample_to_coverage>] [-baq <baq>] [-baqGOP <baqGapOpenPenalty>] [-fixNDN] [-fixMisencodedQuals] [-allowPotentiallyMisencodedQuals] [-OQ] [-DBQ <defaultBaseQualities>] [-PF <performanceLog>] [-BQSR <BQSR>] [-qq <quantize_quals>] [-SQQ <static_quantized_quals>] [-DIQ] [-EOQ] [-preserveQ <preserve_qscores_less_than>] [-globalQScorePrior <globalQScorePrior>] [-secondsBetweenProgressUpdates <secondsBetweenProgressUpdates>] [-S <validation_strictness>] [-rpr] [-kpr] [-sample_rename_mapping_file <sample_rename_mapping_file>] [-U <unsafe>] [-jdk_deflater] [-jdk_inflater] [-disable_auto_index_creation_and_locking_when_reading_rods] [-no_cmdline_in_header] [-sites_only] [-writeFullFormat] [-compress <bam_compression>] [-simplifyBAM] [--disable_bam_indexing] [--generate_md5] [-nt <num_threads>] [-nct <num_cpu_threads_per_data_thread>] [-mte] [-rgbl <read_group_black_list>] [-ped <pedigree>] [-pedString <pedigreeString>] [-pedValidationType <pedigreeValidationType>] [-variant_index_type <variant_index_type>] [-variant_index_parameter <variant_index_parameter>] [-ref_win_stop <reference_window_stop>] [-l <logging_level>] [-log <log_to_file>] [-h] [-version] -T,--analysis_type <analysis_type> Name of the tool to run -args,--arg_file <arg_file> Reads arguments from the specified file -I,--input_file <input_file> Input file containing sequence data (BAM or CRAM) --showFullBamList Emit list of input BAM/CRAM files to log -rbs,--read_buffer_size <read_buffer_size> Number of reads per SAM file to buffer in memory -rf,--read_filter <read_filter> Filters to apply to reads before analysis -drf,--disable_read_filter <disable_read_filter> Read filters to disable -L,--intervals <intervals> One or more genomic intervals over which to operate -XL,--excludeIntervals <excludeIntervals> One or more genomic intervals to exclude from processing -isr,--interval_set_rule <interval_set_rule> Set merging approach to use for combining interval inputs (UNION|INTERSECTION) -im,--interval_merging <interval_merging> Interval merging rule for abutting intervals (ALL| OVERLAPPING_ONLY) -ip,--interval_padding <interval_padding> Amount of padding (in bp) to add to each interval -R,--reference_sequence <reference_sequence> Reference sequence file -ndrs,--nonDeterministicRandomSeed Use a non-deterministic random seed -maxRuntime,--maxRuntime <maxRuntime> Stop execution cleanly as soon as maxRuntime has been reached -maxRuntimeUnits,--maxRuntimeUnits <maxRuntimeUnits> Unit of time used by maxRuntime (NANOSECONDS| MICROSECONDS|MILLISECONDS| SECONDS|MINUTES|HOURS|DAYS) -dt,--downsampling_type <downsampling_type> Type of read downsampling to employ at a given locus (NONE| ALL_READS|BY_SAMPLE) -dfrac,--downsample_to_fraction <downsample_to_fraction> Fraction of reads to downsample to -dcov,--downsample_to_coverage <downsample_to_coverage> Target coverage threshold for downsampling to coverage -baq,--baq <baq> Type of BAQ calculation to apply in the engine (OFF| CALCULATE_AS_NECESSARY| RECALCULATE) -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty> BAQ gap open penalty -fixNDN,--refactor_NDN_cigar_string Reduce NDN elements in CIGAR string -fixMisencodedQuals,--fix_misencoded_quality_scores Fix mis-encoded base quality scores -allowPotentiallyMisencodedQuals,--allow_potentially_misencoded_quality_scores Ignore warnings about base quality score encoding -OQ,--useOriginalQualities Use the base quality scores from the OQ tag -DBQ,--defaultBaseQualities <defaultBaseQualities> Assign a default base quality -PF,--performanceLog <performanceLog> Write GATK runtime performance log to this file -BQSR,--BQSR <BQSR> Input covariates table file for on-the-fly base quality score recalibration -qq,--quantize_quals <quantize_quals> Quantize quality scores to a given number of levels (with -BQSR) -SQQ,--static_quantized_quals <static_quantized_quals> Use static quantized quality scores to a given number of levels (with -BQSR) -DIQ,--disable_indel_quals Disable printing of base insertion and deletion tags (with -BQSR) -EOQ,--emit_original_quals Emit the OQ tag with the original base qualities (with -BQSR) -preserveQ,--preserve_qscores_less_than <preserve_qscores_less_than> Don't recalibrate bases with quality scores less than this threshold (with -BQSR) -globalQScorePrior,--globalQScorePrior <globalQScorePrior> Global Qscore Bayesian prior to use for BQSR -secondsBetweenProgressUpdates,--secondsBetweenProgressUpdates Time interval for process <secondsBetweenProgressUpdates> meter information output (in seconds) -S,--validation_strictness <validation_strictness> How strict should we be with validation (STRICT|LENIENT| SILENT) -rpr,--remove_program_records Remove program records from the SAM header -kpr,--keep_program_records Keep program records in the SAM header -sample_rename_mapping_file,--sample_rename_mapping_file <sample_rename_mapping_file> Rename sample IDs on-the-fly at runtime using the provided mapping file -U,--unsafe <unsafe> Enable unsafe operations: nothing will be checked at runtime (ALLOW_N_CIGAR_READS| ALLOW_UNINDEXED_BAM| ALLOW_UNSET_BAM_SORT_ORDER| NO_READ_ORDER_VERIFICATION| ALLOW_SEQ_DICT_INCOMPATIBILITY| LENIENT_VCF_PROCESSING|ALL) -jdk_deflater,--use_jdk_deflater Use the JDK Deflater instead of the IntelDeflater for writing BAMs -jdk_inflater,--use_jdk_inflater Use the JDK Inflater instead of the IntelInflater for reading BAMs d_locking_when_reading_rods,--disable_auto_index_creation_and_locking_when_reading_rods Disable both auto-generation of index files and index file locking -no_cmdline_in_header,--no_cmdline_in_header Don't include the command line in output VCF headers -sites_only,--sites_only Output sites-only VCF -writeFullFormat,--never_trim_vcf_format_field Always output all the records in VCF FORMAT fields, even if some are missing -compress,--bam_compression <bam_compression> Compression level to use for writing BAM files (0 - 9, higher is more compressed) -simplifyBAM,--simplifyBAM Strip down read content and tags --disable_bam_indexing Turn off on-the-fly creation of indices for output BAM/CRAM files --generate_md5 Enable on-the-fly creation of md5s for output BAM files. -nt,--num_threads <num_threads> Number of data threads to allocate to this analysis -nct,--num_cpu_threads_per_data_thread <num_cpu_threads_per_data_thread> Number of CPU threads to allocate per data thread -mte,--monitorThreadEfficiency Enable threading efficiency monitoring -rgbl,--read_group_black_list <read_group_black_list> Exclude read groups based on tags -ped,--pedigree <pedigree> Pedigree files for samples -pedString,--pedigreeString <pedigreeString> Pedigree string for samples -pedValidationType,--pedigreeValidationType <pedigreeValidationType> Validation strictness for pedigree (STRICT|SILENT) -variant_index_type,--variant_index_type <variant_index_type> Type of IndexCreator to use for VCF/BCF indices (DYNAMIC_SEEK|DYNAMIC_SIZE| LINEAR|INTERVAL) -variant_index_parameter,--variant_index_parameter <variant_index_parameter> Parameter to pass to the VCF/BCF IndexCreator -ref_win_stop,--reference_window_stop <reference_window_stop> Reference window stop -l,--logging_level <logging_level> Set the minimum level of logging -log,--log_to_file <log_to_file> Set the logging location -h,--help Generate the help message -version,--version Output version information annotator VariantAnnotator Annotate variant calls with context information bqsr AnalyzeCovariates Create plots to visualize base recalibration results BaseRecalibrator Detect systematic errors in base quality scores cancer AssignSomaticStatus Assigns somatic status to a set of calls contamination AnnotatePopulationAFWalker Given a input VCF representing a collection of populations, split the input into each population, and annotate each record with population allele frequencies ContEst Estimate cross-sample contamination coverage CallableLoci Collect statistics on callable, uncallable, poorly mapped, and other parts of the genome CompareCallableLoci Compare callability statistics DepthOfCoverage Assess sequence coverage by a wide array of metrics, partitioned by sample, read group, or library GCContentByInterval Calculates the GC content of the reference sequence for each interval diagnosetargets DiagnoseTargets Analyze coverage distribution and validate read mates per interval and per sample diagnostics ErrorRatePerCycle Compute the read error rate per position FindCoveredIntervals Outputs a list of intervals that are covered to or above a given threshold ReadGroupProperties Collect statistics about read groups and their properties ReadLengthDistribution Collect read length statistics diffengine DiffObjects A generic engine for comparing tree-structured objects examples GATKPaperGenotyper Simple Bayesian genotyper used in the original GATK paper fasta FastaAlternateReferenceMaker Generate an alternative reference sequence over the specified interval FastaReferenceMaker Create a subset of a FASTA reference sequence FastaStats Calculate basic statistics about the reference sequence itself filters VariantFiltration Filter variant calls based on INFO and FORMAT annotations genotyper UnifiedGenotyper Call SNPs and indels on a per-locus basis haplotypecaller HaplotypeCaller Call germline SNPs and indels via local re-assembly of haplotypes HaplotypeResolver Haplotype-based resolution of variants in separate callsets. indels IndelRealigner Perform local realignment of reads around indels LeftAlignIndels Left-align indels within reads in a bam file RealignerTargetCreator Define intervals to target for local realignment m2 MuTect2 Call somatic SNPs and indels via local re-assembly of haplotypes missing QualifyMissingIntervals Collect quality metrics for a set of intervals phasing PhaseByTransmission Compute the most likely genotype combination and phasing for trios and parent/child pairs ReadBackedPhasing Annotate physical phasing information qc CheckPileup Compare GATK's internal pileup to a reference Samtools pileup CountBases Count the number of bases in a set of reads CountIntervals Count contiguous regions in an interval list CountLoci Count the total number of covered loci CountMales Count the number of reads seen from male samples CountReadEvents Count the number of read events CountReads Count the number of reads CountRODs Count the number of ROD objects encountered CountRODsByRef Count the number of ROD objects encountered along the reference CountTerminusEvent Count the number of reads ending in insertions, deletions or soft-clips ErrorThrowing A walker that simply throws errors. FlagStat Collect statistics about sequence reads based on their SAM flags Pileup Print read alignments in Pileup-style format PrintRODs Print out all of the RODs in the input data set QCRef Quality control for the reference fasta ReadClippingStats Collect read clipping statistics readutils ClipReads Read clipping based on quality, position or sequence matching PrintReads Write out sequence read data (for filtering, merging, subsetting etc) SplitSamFile Split a BAM file by sample rnaseq ASEReadCounter Calculate read counts per allele for allele-specific expression analysis SplitNCigarReads Splits reads that contain Ns in their CIGAR string simulatereads SimulateReadsForVariants Generate simulated reads for variants validationsiteselector ValidationSiteSelector Randomly select variant records according to specified options varianteval VariantEval General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more) variantrecalibration ApplyRecalibration Apply a score cutoff to filter variants based on a recalibration table VariantRecalibrator Build a recalibration model to score variant quality for filtering purposes variantutils CalculateGenotypePosteriors Calculate genotype posterior likelihoods given panel data CombineGVCFs Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file CombineVariants Combine variant records from different sources GenotypeConcordance Genotype concordance between two callsets GenotypeGVCFs Perform joint genotyping on gVCF files produced by HaplotypeCaller LeftAlignAndTrimVariants Left-align indels in a variant callset RandomlySplitVariants Randomly split variants into different sets RegenotypeVariants Regenotypes the variants from a VCF containing PLs or GLs. SelectHeaders Selects headers from a VCF source SelectVariants Select a subset of variants from a larger callset ValidateVariants Validate a VCF file with an extra strict set of criteria VariantsToAllelicPrimitives Simplify multi-nucleotide variants (MNPs) into more basic/primitive alleles. VariantsToBinaryPed Convert VCF to binary pedigree file VariantsToTable Extract specific fields from a VCF file to a tab-delimited table VariantsToVCF Convert variants from other file formats to VCF format
Installation
Source code is obtained from GATK
System
64-bit Linux